Add conftest and doctest

.travis.yml

@@ -9,7 +9,7 @@ cache:
 env:
   global:
     # Directory where tests are run from
-    - TEST_DIR=/tmp/sklearn
+    - TEST_DIR=/tmp/skopt
     - OMP_NUM_THREADS=4
     - OPENBLAS_NUM_THREADS=4
 
@@ -57,6 +57,7 @@ script:
     then pytest --cov=skopt --durations=10; else
     pytest --durations=10;
     fi
+- bash build_tools/travis/test_docs.sh
 
 after_success:
   - if [ ${COVERAGE} == "true" ]; then

Makefile

@@ -0,0 +1,67 @@
+# simple makefile to simplify repetitive build env management tasks under posix
+
+# caution: testing won't work on windows, see README
+
+PYTHON ?= python
+CYTHON ?= cython
+PYTEST ?= pytest
+CTAGS ?= ctags
+
+# skip doctests on 32bit python
+BITS := $(shell python -c 'import struct; print(8 * struct.calcsize("P"))')
+
+all: clean inplace test
+
+clean-ctags:
+	rm -f tags
+
+clean: clean-ctags
+	$(PYTHON) setup.py clean
+	rm -rf dist
+	# TODO: Remove in when all modules are removed.
+	$(PYTHON) sklearn/_build_utils/deprecated_modules.py
+
+in: inplace # just a shortcut
+inplace:
+	$(PYTHON) setup.py build_ext -i
+
+test-code: in
+	$(PYTEST) --showlocals -v skopt --durations=20
+test-sphinxext:
+	$(PYTEST) --showlocals -v doc/sphinxext/
+test-doc:
+ifeq ($(BITS),64)
+	$(PYTEST) $(shell find doc -name '*.rst' | sort)
+endif
+test-code-parallel: in
+	$(PYTEST) -n auto --showlocals -v skopt --durations=20
+
+test-coverage:
+	rm -rf coverage .coverage
+	$(PYTEST) skopt --showlocals -v --cov=sklearn --cov-report=html:coverage
+test-coverage-parallel:
+	rm -rf coverage .coverage .coverage.*
+	$(PYTEST) skopt -n auto --showlocals -v --cov=sklearn --cov-report=html:coverage
+
+test: test-code test-sphinxext test-doc
+
+trailing-spaces:
+	find skopt -name "*.py" -exec perl -pi -e 's/[ \t]*$$//' {} \;
+
+ctags:
+	# make tags for symbol based navigation in emacs and vim
+	# Install with: sudo apt-get install exuberant-ctags
+	$(CTAGS) --python-kinds=-i -R skopt
+
+doc: inplace
+	$(MAKE) -C doc html
+
+doc-noplot: inplace
+	$(MAKE) -C doc html-noplot
+
+code-analysis:
+	flake8 sklearn | grep -v __init__ | grep -v external
+	pylint -E -i y skopt/ -d E1103,E0611,E1101
+
+flake8-diff:
+	./build_tools/circle/linting.sh

build_tools/travis/after_success.sh

@@ -0,0 +1,19 @@
+#!/bin/bash
+# This script is meant to be called by the "after_success" step defined in
+# .travis.yml. See https://docs.travis-ci.com/ for more details.
+
+# License: 3-clause BSD
+
+set -e
+
+if [[ "$COVERAGE" == "true" ]]; then
+    # Need to run codecov from a git checkout, so we copy .coverage
+    # from TEST_DIR where pytest has been run
+    cp $TEST_DIR/.coverage $TRAVIS_BUILD_DIR
+
+    # Ignore codecov failures as the codecov server is not
+    # very reliable but we don't want travis to report a failure
+    # in the github UI just because the coverage report failed to
+    # be published.
+    codecov --root $TRAVIS_BUILD_DIR || echo "codecov upload failed"
+fi

build_tools/travis/test_docs.sh

@@ -0,0 +1,6 @@
+#!/bin/bash
+
+set -e
+set -x
+
+make test-doc

build_tools/travis/test_script.sh

@@ -0,0 +1,51 @@
+#!/bin/bash
+# This script is meant to be called by the "script" step defined in
+# .travis.yml. See https://docs.travis-ci.com/ for more details.
+# The behavior of the script is controlled by environment variabled defined
+# in the .travis.yml in the top level folder of the project.
+
+# License: 3-clause BSD
+
+set -e
+
+python --version
+python -c "import numpy; print('numpy %s' % numpy.__version__)"
+python -c "import scipy; print('scipy %s' % scipy.__version__)"
+python -c "\
+try:
+    import sklearn
+    print('sklearn %s' % sklearn.__version__)
+except ImportError:
+    pass
+"
+python -c "import multiprocessing as mp; print('%d CPUs' % mp.cpu_count())"
+
+run_tests() {
+    TEST_CMD="pytest --showlocals --durations=20 --pyargs"
+
+    # Get into a temp directory to run test from the installed scikit-learn and
+    # check if we do not leave artifacts
+    mkdir -p $TEST_DIR
+    # We need the setup.cfg for the pytest settings
+    cp setup.cfg $TEST_DIR
+    cd $TEST_DIR
+
+    # Skip tests that require large downloads over the network to save bandwidth
+    # usage as travis workers are stateless and therefore traditional local
+    # disk caching does not work.
+    export SKOPT_SKIP_NETWORK_TESTS=1
+
+    if [[ "$COVERAGE" == "true" ]]; then
+        TEST_CMD="$TEST_CMD --cov sklearn"
+    fi
+
+    if [[ -n "$CHECK_WARNINGS" ]]; then
+        TEST_CMD="$TEST_CMD -Werror::DeprecationWarning -Werror::FutureWarning"
+    fi
+
+    set -x  # print executed commands to the terminal
+
+    $TEST_CMD skopt
+}
+
+run_tests

conftest.py

@@ -0,0 +1,83 @@
+# Even if empty this file is useful so that when running from the root folder
+# ./sklearn is added to sys.path by pytest. See
+# https://docs.pytest.org/en/latest/pythonpath.html for more details.  For
+# example, this allows to build extensions in place and run pytest
+# doc/modules/clustering.rst and use sklearn from the local folder rather than
+# the one from site-packages.
+
+import platform
+import sys
+from distutils.version import LooseVersion
+import os
+
+import pytest
+from _pytest.doctest import DoctestItem
+from sklearn.utils import _IS_32BIT
+
+
+PYTEST_MIN_VERSION = '3.3.0'
+
+if LooseVersion(pytest.__version__) < PYTEST_MIN_VERSION:
+    raise ImportError('Your version of pytest is too old, you should have '
+                      'at least pytest >= {} installed.'
+                      .format(PYTEST_MIN_VERSION))
+
+
+def pytest_addoption(parser):
+    parser.addoption("--skip-network", action="store_true", default=False,
+                     help="skip network tests")
+
+
+def pytest_collection_modifyitems(config, items):
+    # FeatureHasher is not compatible with PyPy
+    if platform.python_implementation() == 'PyPy':
+        skip_marker = pytest.mark.skip(
+            reason='FeatureHasher is not compatible with PyPy')
+        for item in items:
+            if item.name.endswith(('_hash.FeatureHasher',
+                                   'text.HashingVectorizer')):
+                item.add_marker(skip_marker)
+
+    # Skip tests which require internet if the flag is provided
+    if config.getoption("--skip-network"):
+        skip_network = pytest.mark.skip(
+            reason="test requires internet connectivity")
+        for item in items:
+            if "network" in item.keywords:
+                item.add_marker(skip_network)
+
+    # numpy changed the str/repr formatting of numpy arrays in 1.14. We want to
+    # run doctests only for numpy >= 1.14.
+    skip_doctests = False
+    try:
+        import numpy as np
+        if LooseVersion(np.__version__) < LooseVersion('1.14'):
+            reason = 'doctests are only run for numpy >= 1.14'
+            skip_doctests = True
+        elif _IS_32BIT:
+            reason = ('doctest are only run when the default numpy int is '
+                      '64 bits.')
+            skip_doctests = True
+        elif sys.platform.startswith("win32"):
+            reason = ("doctests are not run for Windows because numpy arrays "
+                      "repr is inconsistent across platforms.")
+            skip_doctests = True
+    except ImportError:
+        pass
+
+    if skip_doctests:
+        skip_marker = pytest.mark.skip(reason=reason)
+
+        for item in items:
+            if isinstance(item, DoctestItem):
+                item.add_marker(skip_marker)
+
+
+def pytest_configure(config):
+    import sys
+    sys._is_pytest_session = True
+
+
+def pytest_unconfigure(config):
+    import sys
+    del sys._is_pytest_session

doc/Makefile

@@ -1,22 +1,110 @@
-# Minimal makefile for Sphinx documentation
+# Makefile for Sphinx documentation
 #
 
 # You can set these variables from the command line.
-SPHINXOPTS    = -W --keep-going
-SPHINXBUILD   = sphinx-build
-SPHINXPROJ    = scikit-optimize
-SOURCEDIR     = source
-BUILDDIR      = build
+SPHINXOPTS    = -j auto
+SPHINXBUILD  ?= sphinx-build
+PAPER         =
+BUILDDIR      = _build
+ifneq ($(EXAMPLES_PATTERN),)
+    EXAMPLES_PATTERN_OPTS := -D sphinx_gallery_conf.filename_pattern="$(EXAMPLES_PATTERN)"
+endif
+
+# Internal variables.
+PAPEROPT_a4     = -D latex_paper_size=a4
+PAPEROPT_letter = -D latex_paper_size=letter
+ALLSPHINXOPTS   = -T -d $(BUILDDIR)/doctrees $(PAPEROPT_$(PAPER)) $(SPHINXOPTS)\
+    $(EXAMPLES_PATTERN_OPTS) .
+
+
+.PHONY: help clean html dirhtml pickle json latex latexpdf changes linkcheck doctest optipng
+
+all: html-noplot
 
-# Put it first so that "make" without argument is like "make help".
 help:
-	@$(SPHINXBUILD) -M help "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+	@echo "Please use \`make <target>' where <target> is one of"
+	@echo "  html      to make standalone HTML files"
+	@echo "  dirhtml   to make HTML files named index.html in directories"
+	@echo "  pickle    to make pickle files"
+	@echo "  json      to make JSON files"
+	@echo "  latex     to make LaTeX files, you can set PAPER=a4 or PAPER=letter"
+	@echo "  latexpdf   to make LaTeX files and run them through pdflatex"
+	@echo "  changes   to make an overview of all changed/added/deprecated items"
+	@echo "  linkcheck to check all external links for integrity"
+	@echo "  doctest   to run all doctests embedded in the documentation (if enabled)"
+
+clean:
+	-rm -rf $(BUILDDIR)/*
+	-rm -rf auto_examples/
+	-rm -rf generated/*
+	-rm -rf modules/generated/
+
+html:
+	# These two lines make the build a bit more lengthy, and the
+	# the embedding of images more robust
+	rm -rf $(BUILDDIR)/html/_images
+	#rm -rf _build/doctrees/
+	$(SPHINXBUILD) -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html"
+
+html-noplot:
+	$(SPHINXBUILD) -D plot_gallery=0 -b html $(ALLSPHINXOPTS) $(BUILDDIR)/html
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/html."
+
+dirhtml:
+	$(SPHINXBUILD) -b dirhtml $(ALLSPHINXOPTS) $(BUILDDIR)/dirhtml
+	@echo
+	@echo "Build finished. The HTML pages are in $(BUILDDIR)/dirhtml."
+
+pickle:
+	$(SPHINXBUILD) -b pickle $(ALLSPHINXOPTS) $(BUILDDIR)/pickle
+	@echo
+	@echo "Build finished; now you can process the pickle files."
+
+json:
+	$(SPHINXBUILD) -b json $(ALLSPHINXOPTS) $(BUILDDIR)/json
+	@echo
+	@echo "Build finished; now you can process the JSON files."
+
+latex:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo
+	@echo "Build finished; the LaTeX files are in $(BUILDDIR)/latex."
+	@echo "Run \`make' in that directory to run these through (pdf)latex" \
+	      "(use \`make latexpdf' here to do that automatically)."
+
+latexpdf:
+	$(SPHINXBUILD) -b latex $(ALLSPHINXOPTS) $(BUILDDIR)/latex
+	@echo "Running LaTeX files through pdflatex..."
+	make -C $(BUILDDIR)/latex all-pdf
+	@echo "pdflatex finished; the PDF files are in $(BUILDDIR)/latex."
+
+changes:
+	$(SPHINXBUILD) -b changes $(ALLSPHINXOPTS) $(BUILDDIR)/changes
+	@echo
+	@echo "The overview file is in $(BUILDDIR)/changes."
+
+linkcheck:
+	$(SPHINXBUILD) -b linkcheck $(ALLSPHINXOPTS) $(BUILDDIR)/linkcheck
+	@echo
+	@echo "Link check complete; look for any errors in the above output " \
+	      "or in $(BUILDDIR)/linkcheck/output.txt."
+
+doctest:
+	$(SPHINXBUILD) -b doctest $(ALLSPHINXOPTS) $(BUILDDIR)/doctest
+	@echo "Testing of doctests in the sources finished, look at the " \
+	      "results in $(BUILDDIR)/doctest/output.txt."
+
+# download-data:
+# 	python -c "from sklearn.datasets._lfw import _check_fetch_lfw; _check_fetch_lfw()"
 
-.PHONY: help Makefile
+# Optimize PNG files. Needs OptiPNG. Change the -P argument to the number of
+# cores you have available, so -P 64 if you have a real computer ;)
+optipng:
+	find _build auto_examples */generated -name '*.png' -print0 \
+	  | xargs -0 -n 1 -P 4 optipng -o10
 
-# Catch-all target: route all unknown targets to Sphinx using the new
-# "make mode" option.  $(O) is meant as a shortcut for $(SPHINXOPTS).
-%: Makefile
-    mkdir ./source/notebooks
-    cp -r ../examples/* ./source/notebooks
-	@$(SPHINXBUILD) -M $@ "$(SOURCEDIR)" "$(BUILDDIR)" $(SPHINXOPTS) $(O)
+dist: html latexpdf
+	cp _build/latex/user_guide.pdf _build/html/_downloads/scikit-optimize-docs.pdf